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Volumn 1125, Issue , 2014, Pages 119-129

Accurate mapping of cleavage and polyadenylation sites by 3′ region extraction and deep sequencing

Author keywords

Cleavage and polyadenylation; Deep sequencing; Gene expression; PolyA site; RNA seq

Indexed keywords

MESSENGER RNA; POLYADENYLIC ACID;

EID: 84908376935     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-971-0_10     Document Type: Chapter
Times cited : (19)

References (23)
  • 1
    • 0036364652 scopus 로고    scopus 로고
    • A history of poly A sequences: From formation to factors to function
    • Edmonds M (2002) A history of poly A sequences: from formation to factors to function. Prog Nucleic Acid Res Mol Biol 71:285–389.
    • (2002) Prog Nucleic Acid Res Mol Biol , vol.71 , pp. 285-389
    • Edmonds, M.1
  • 2
    • 0030784958 scopus 로고    scopus 로고
    • Mechanism and regulation of mRNA polyadenylation
    • Colgan DF, Manley JL (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev 11:2755–2766.
    • (1997) Genes Dev , vol.11 , pp. 2755-2766
    • Colgan, D.F.1    Manley, J.L.2
  • 3
    • 80052447253 scopus 로고    scopus 로고
    • Ending the message: Poly(A) signals then and now
    • Proudfoot NJ (2011) Ending the message: poly(A) signals then and now. Genes Dev 25:1770–1782.
    • (2011) Genes Dev , vol.25 , pp. 1770-1782
    • Proudfoot, N.J.1
  • 4
    • 84862526272 scopus 로고    scopus 로고
    • Signals for premRNA cleavage and polyadenylation
    • Tian B, Graber JH (2012) Signals for premRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA 3(3):385–396.
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , Issue.3 , pp. 385-396
    • Tian, B.1    Graber, J.H.2
  • 5
    • 13744254695 scopus 로고    scopus 로고
    • A largescale analysis of mRNA polyadenylation of human and mouse genes
    • Tian B, Hu J, Zhang H et al (2005) A largescale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33:201–212.
    • (2005) Nucleic Acids Res , vol.33 , pp. 201-212
    • Tian, B.1    Hu, J.2    Zhang, H.3
  • 6
    • 80052979140 scopus 로고    scopus 로고
    • Mechanisms and consequences of alternative polyadenylation
    • di Giammartino DC, Nishida K, Manley JL (2011) Mechanisms and consequences of alternative polyadenylation. Mol Cell 43:853–866.
    • (2011) Mol Cell , vol.43 , pp. 853-866
    • Di Giammartino, D.C.1    Nishida, K.2    Manley, J.L.3
  • 7
    • 84857772692 scopus 로고    scopus 로고
    • Alternative mRNA polyadenylation in eukaryotes: An effective regulator of gene expression
    • Lutz CS, Moreira A (2011) Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. WIREs RNA 2:23–31.
    • (2011) Wires RNA , vol.2 , pp. 23-31
    • Lutz, C.S.1    Moreira, A.2
  • 8
    • 33646950851 scopus 로고    scopus 로고
    • Biased alternative polyadenylation in human tissues
    • Zhang H, Lee JY, Tian B (2005) Biased alternative polyadenylation in human tissues. Genome Biol 6:R100.
    • (2005) Genome Biol , vol.6
    • Zhang, H.1    Lee, J.Y.2    Tian, B.3
  • 9
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1    Sandberg, R.2    Luo, S.3
  • 10
    • 66049104920 scopus 로고    scopus 로고
    • Progressive lengthening of 3′untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
    • Ji Z, Lee JY, Pan Z et al (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106:7028–7033.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 7028-7033
    • Ji, Z.1    Lee, J.Y.2    Pan, Z.3
  • 11
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 3′untranslated regions and fewer microRNA target sites
    • Sandberg R, Neilson JR, Sarma A et al (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320:1643–1647.
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3
  • 12
    • 68749113985 scopus 로고    scopus 로고
    • Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
    • Mayr C, Bartel DP (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138:673–684.
    • (2009) Cell , vol.138 , pp. 673-684
    • Mayr, C.1    Bartel, D.P.2
  • 13
    • 73649139638 scopus 로고    scopus 로고
    • Global changes in processing of mRNA 3′untranslated regions characterize clinically distinct cancer subtypes
    • Singh P, Alley TL, Wright SM et al (2009) Global changes in processing of mRNA 3′ untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 69: 9422–9430.
    • (2009) Cancer Res , vol.69 , pp. 9422-9430
    • Singh, P.1    Alley, T.L.2    Wright, S.M.3
  • 14
    • 57649211993 scopus 로고    scopus 로고
    • Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection
    • Flavell SW, Kim TK, Gray JM et al (2008) Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60:1022–1038.
    • (2008) Neuron , vol.60 , pp. 1022-1038
    • Flavell, S.W.1    Kim, T.K.2    Gray, J.M.3
  • 15
    • 33846059244 scopus 로고    scopus 로고
    • PolyA_DB 2: MRNA polyadenylation sites in vertebrate genes
    • Lee JY, Yeh I, Park JY et al (2007) PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 35:D165–D168.
    • (2007) Nucleic Acids Res , vol.35 , pp. D165-D168
    • Lee, J.Y.1    Yeh, I.2    Park, J.Y.3
  • 16
    • 24644442199 scopus 로고    scopus 로고
    • PACdb: PolyA cleavage site and 3′-UTR database
    • Brockman JM, Singh P, Liu D et al (2005) PACdb: polyA cleavage site and 3′-UTR database. Bioinformatics 21:3691–3693.
    • (2005) Bioinformatics , vol.21 , pp. 3691-3693
    • Brockman, J.M.1    Singh, P.2    Liu, D.3
  • 17
    • 0037197827 scopus 로고    scopus 로고
    • Oligo(DT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
    • Nam DK, Lee S, Zhou G et al (2002) Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci U S A 99:6152–6156.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 6152-6156
    • Nam, D.K.1    Lee, S.2    Zhou, G.3
  • 18
    • 79955587252 scopus 로고    scopus 로고
    • The nuclear RNA polymerase II surveillance system targets polymerase III transcripts
    • Wlotzka W, Kudla G, Granneman S et al (2011) The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J 30:1790–1803.
    • (2011) EMBO J , vol.30 , pp. 1790-1803
    • Wlotzka, W.1    Kudla, G.2    Granneman, S.3
  • 19
    • 78650433004 scopus 로고    scopus 로고
    • Polyadenylation and beyond: Emerging roles for noncanonical poly(A) polymerases
    • Schmidt MJ, Norbury CJ (2010) Polyadenylation and beyond: emerging roles for noncanonical poly(A) polymerases. Wiley Interdiscip Rev RNA 1:142–151.
    • (2010) Wiley Interdiscip Rev RNA , vol.1 , pp. 142-151
    • Schmidt, M.J.1    Norbury, C.J.2
  • 20
    • 84873405541 scopus 로고    scopus 로고
    • Analysis of alternative cleavage and polyadenylation by 3′region extraction and deep sequencing
    • Hoque M, Ji Z, Zheng D et al (2013) Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing. Nat Methods 10:133–139.
    • (2013) Nat Methods , vol.10 , pp. 133-139
    • Hoque, M.1    Ji, Z.2    Zheng, D.3
  • 21
    • 84859210032 scopus 로고    scopus 로고
    • Fast gappedread alignment with Bowtie 2
    • Langmead B, Salzberg SL (2012) Fast gappedread alignment with Bowtie 2. Nat Methods 9:357–359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 22
    • 82255185567 scopus 로고    scopus 로고
    • Identifi cation and remediation of biases in the activity of RNA ligases in small- RNA deep sequencing
    • Jayaprakash AD, Jabado O, Brown BD et al (2011) Identifi cation and remediation of biases in the activity of RNA ligases in small- RNA deep sequencing. Nucleic Acids Res 39:e141.
    • (2011) Nucleic Acids Res , vol.39
    • Jayaprakash, A.D.1    Jabado, O.2    Brown, B.D.3
  • 23
    • 84860198538 scopus 로고    scopus 로고
    • Structural bias in T4 RNA ligase-mediated 3′-adapter ligation
    • Zhuang F, Fuchs RT, Sun Z et al (2012) Structural bias in T4 RNA ligase-mediated 3′-adapter ligation. Nucleic Acids Res 40:e54.
    • (2012) Nucleic Acids Res , vol.40
    • Zhuang, F.1    Fuchs, R.T.2    Sun, Z.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.